The Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) will apply a scalable, high throughput DNA sequencing process in a co- operative effort for the generation of a complete human genomic reference sequence, and the fulfillment of the aims of the NIH/DOE Human Genome Project five year plan. In the first year of the capacity to produce raw DNA sequencing reads, and finishing of DNA sequence to high quality, will each be aggressively expanded. The increased raw data production will rely heavily on an automated platform that integrates commercially available devices, machines developed locally, and established BCM-HGSC sequencing protocols. New Perkin-Elmer 3700 capillary DNA sequencers will be used to boost throughput and the entire activity will be housed in newly renovated BCM-HGSC space. Finishing rates will be increased by a combination of informatics tools, a double stranded plasmid system, and automatic clone re-arraying. The sequencing will generate at least 44 Mb of high quality data in year one, 100 Mb/year in year two, and 120 Mb/year thereafter. Additional sequence coverage at 4.5-5.0 X, and at 9.0-10 X will also be generated, so that more than 120 Mb of additional genome coverage will be achieved in the first year. The sequence 'drafting' will continue until the end of 2001, when the emphasis will shift towards deeper coverage of all clones in the sequence pipeline. By the end of 2003 there will be approximately 1.2 Gb of sequence coverage, with a minimum of 530 Mb at high quality and the remainder 'near finished'. With the proposed increases in finishing efficiency, the remaining 700 Mb of the 1.2 Gb will also be finished. The minimal plan calls for completion of mapped clones representing all human Chromosome 12 (120 Mb), Chromosome 3 (240 Mb) and portions of Chromosome X (40Mb). Subsequent targets, beyond this 400 Mb, will depend on the community mapping and sequencing strategies. A modest amount of murine sequence will be completed during this time, and any excess capacity resulting from other successful community efforts for human DNA sequencing will free the BCM-HGSC resource to focus further on model organisms.